The Japanese government has statistics of people's houses. According to its 2014 statistics, 70% of Tokyo residents live in flats or apartment houses (not stand-alone house, not detached house). The figure below shows the ratio of flats/apartment houses by prefecture.
Red means most of people live in flats, blue means many live in stand-alone houses.

Obviously the rate is higher in big cities, like Tokyo, Osaka, Nagoya, Yokohama, Fukuoka.
Table: Ratio of Flat/Apartment house by Prefecture in 2014 (unit: %)
| Prefecture | Ratio of flats |
| Tokyo | 70.0 |
| Kanagawa | 56.1 |
| Okinawa | 55.9 |
| Osaka | 55.2 |
| Fukuoka | 51.1 |
| Hyogo | 46.6 |
| Aichi | 46.4 |
| Chiba | 43.8 |
| Average | 42.4 |
| Saitama | 42.3 |
| Hokkaido | 42.0 |
| Miyagi | 41.5 |
| Kyoto | 40.7 |
| Hiroshima | 39.1 |
| Oita | 33.6 |
| Kumamoto | 31.7 |
| Shizuoka | 30.4 |
| Nagasaki | 29.6 |
| Kagoshima | 28.5 |
| Shiga | 28.0 |
| Nara | 28.0 |
| Yamaguchi | 27.8 |
| Okayama | 27.4 |
| Kochi | 27.4 |
| Kagawa | 27.1 |
| Ishikawa | 26.7 |
| Ehime | 26.5 |
| Fukushima | 26.2 |
| Miyazaki | 26.1 |
| Tochigi | 24.6 |
| Tokushima | 24.5 |
| Ibaraki | 24.4 |
| Yamanashi | 23.8 |
| Saga | 23.7 |
| Tottori | 23.6 |
| Gunma | 23.3 |
| Iwate | 22.9 |
| Mie | 22.7 |
| Gifu | 22.4 |
| Shimane | 22.3 |
| Niigata | 21.8 |
| Nagano | 21.0 |
| Aomori | 19.7 |
| Fukui | 19.5 |
| Wakayama | 19.0 |
| Toyama | 18.9 |
| Yamagata | 18.4 |
| Akita | 17.3 |
I was surprised that many Okinawa people live in flats. Okinawa is not a big city.
Source is Statistics Bureau.
www.stat.go.jp/data/jyutaku/2013/10_2.htm
www.stat.go.jp/data/jyutaku/2013/pdf/giy12.pdf
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